Integration of Tyser and Zhai datasets

We integrate the public datasets Tyser (1195 cells, Human) and Zhai CS8 (11629 cells, Macaca) following both the standard CCA integration approach and the RPCA approach.

CCA Integrated data

studies integrated

original annotation from each study

Clustering resolutions

Visualization of the different clustering resolutions of the integrated reference

Clustering the cells

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

Dotplots of marker genes

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

Cell proportions per cluster - original annotation

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

RPCA Integrated data

studies integrated

original annotation from each study

Clustering resolutions

Visualization of the different clustering resolutions of the integrated reference

Clustering the cells

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

Dotplots of marker genes

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

Cell proportions per cluster - original annotation

integrated_snn_res.0.2

integrated_snn_res.0.4

integrated_snn_res.0.6

integrated_snn_res.0.8

integrated_snn_res.1

integrated_snn_res.1.2

integrated_snn_res.1.4

sessionInfo

## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Rocky Linux 8.7 (Green Obsidian)
## 
## Matrix products: default
## BLAS/LAPACK: /flask/apps/eb/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] viridis_0.6.4      viridisLite_0.4.2  clustree_0.5.0     ggraph_2.1.0      
##  [5] cowplot_1.1.1      scales_1.2.1       ggpubr_0.6.0       patchwork_1.1.2   
##  [9] SeuratObject_4.1.3 Seurat_4.3.0.1     glue_1.6.2         DT_0.28           
## [13] lubridate_1.9.2    forcats_1.0.0      stringr_1.5.0      dplyr_1.1.2       
## [17] purrr_1.0.1        readr_2.1.4        tidyr_1.3.0        tibble_3.2.1      
## [21] ggplot2_3.4.2      tidyverse_2.0.0    here_1.0.1        
## 
## loaded via a namespace (and not attached):
##   [1] readxl_1.4.3           backports_1.4.1        plyr_1.8.8            
##   [4] igraph_1.5.0.1         lazyeval_0.2.2         sp_2.0-0              
##   [7] splines_4.2.0          listenv_0.9.0          scattermore_1.2       
##  [10] digest_0.6.33          htmltools_0.5.5        fansi_1.0.4           
##  [13] checkmate_2.2.0        magrittr_2.0.3         tensor_1.5            
##  [16] cluster_2.1.4          ROCR_1.0-11            tzdb_0.4.0            
##  [19] globals_0.16.2         graphlayouts_1.0.0     matrixStats_1.0.0     
##  [22] timechange_0.2.0       spatstat.sparse_3.0-2  colorspace_2.1-0      
##  [25] ggrepel_0.9.3          xfun_0.39              jsonlite_1.8.7        
##  [28] progressr_0.13.0       spatstat.data_3.0-1    survival_3.5-5        
##  [31] zoo_1.8-12             polyclip_1.10-4        gtable_0.3.3          
##  [34] leiden_0.4.3           car_3.1-2              future.apply_1.11.0   
##  [37] abind_1.4-5            rstatix_0.7.2          spatstat.random_3.1-5 
##  [40] miniUI_0.1.1.1         Rcpp_1.0.11            xtable_1.8-4          
##  [43] reticulate_1.30        htmlwidgets_1.6.2      httr_1.4.6            
##  [46] RColorBrewer_1.1-3     ellipsis_0.3.2         ica_1.0-3             
##  [49] pkgconfig_2.0.3        farver_2.1.1           sass_0.4.7            
##  [52] uwot_0.1.16            deldir_1.0-9           utf8_1.2.3            
##  [55] labeling_0.4.2         tidyselect_1.2.0       rlang_1.1.1           
##  [58] reshape2_1.4.4         later_1.3.1            cellranger_1.1.0      
##  [61] munsell_0.5.0          tools_4.2.0            cachem_1.0.8          
##  [64] cli_3.6.1              generics_0.1.3         broom_1.0.5           
##  [67] ggridges_0.5.4         evaluate_0.21          fastmap_1.1.1         
##  [70] yaml_2.3.7             goftest_1.2-3          knitr_1.43            
##  [73] fitdistrplus_1.1-11    tidygraph_1.2.3        RANN_2.6.1            
##  [76] pbapply_1.7-2          future_1.33.0          nlme_3.1-162          
##  [79] mime_0.12              compiler_4.2.0         rstudioapi_0.15.0     
##  [82] plotly_4.10.1          png_0.1-8              ggsignif_0.6.4        
##  [85] spatstat.utils_3.0-3   tweenr_2.0.2           bslib_0.5.0           
##  [88] stringi_1.7.12         highr_0.10             lattice_0.21-8        
##  [91] Matrix_1.6-0           vctrs_0.6.3            pillar_1.9.0          
##  [94] lifecycle_1.0.3        spatstat.geom_3.2-4    lmtest_0.9-40         
##  [97] jquerylib_0.1.4        RcppAnnoy_0.0.21       data.table_1.14.8     
## [100] irlba_2.3.5.1          httpuv_1.6.11          R6_2.5.1              
## [103] promises_1.2.0.1       KernSmooth_2.23-22     gridExtra_2.3         
## [106] parallelly_1.36.0      codetools_0.2-19       MASS_7.3-60           
## [109] rprojroot_2.0.3        withr_2.5.0            sctransform_0.3.5     
## [112] parallel_4.2.0         hms_1.1.3              grid_4.2.0            
## [115] rmarkdown_2.23         carData_3.0-5          Rtsne_0.16            
## [118] spatstat.explore_3.2-1 ggforce_0.4.1          shiny_1.7.4